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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 11-65882229-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=65882229&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 65882229,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001335.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile",
"transcript": "NM_001335.4",
"protein_id": "NP_001326.3",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 376,
"cds_start": 341,
"cds_end": null,
"cds_length": 1131,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000307886.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001335.4"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile",
"transcript": "ENST00000307886.8",
"protein_id": "ENSP00000311300.3",
"transcript_support_level": 1,
"aa_start": 114,
"aa_end": null,
"aa_length": 376,
"cds_start": 341,
"cds_end": null,
"cds_length": 1131,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001335.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000307886.8"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "c.431G>T",
"hgvs_p": "p.Ser144Ile",
"transcript": "ENST00000680443.1",
"protein_id": "ENSP00000505179.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 406,
"cds_start": 431,
"cds_end": null,
"cds_length": 1221,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680443.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile",
"transcript": "ENST00000894913.1",
"protein_id": "ENSP00000564972.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 384,
"cds_start": 341,
"cds_end": null,
"cds_length": 1155,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894913.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "c.362G>T",
"hgvs_p": "p.Ser121Ile",
"transcript": "ENST00000894912.1",
"protein_id": "ENSP00000564971.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 383,
"cds_start": 362,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000894912.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile",
"transcript": "ENST00000528419.6",
"protein_id": "ENSP00000436568.1",
"transcript_support_level": 2,
"aa_start": 114,
"aa_end": null,
"aa_length": 364,
"cds_start": 341,
"cds_end": null,
"cds_length": 1095,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000528419.6"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile",
"transcript": "ENST00000680670.1",
"protein_id": "ENSP00000504913.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 359,
"cds_start": 341,
"cds_end": null,
"cds_length": 1080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680670.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile",
"transcript": "ENST00000526034.2",
"protein_id": "ENSP00000434267.2",
"transcript_support_level": 5,
"aa_start": 114,
"aa_end": null,
"aa_length": 349,
"cds_start": 341,
"cds_end": null,
"cds_length": 1050,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000526034.2"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "c.227G>T",
"hgvs_p": "p.Ser76Ile",
"transcript": "ENST00000679584.1",
"protein_id": "ENSP00000505022.1",
"transcript_support_level": null,
"aa_start": 76,
"aa_end": null,
"aa_length": 338,
"cds_start": 227,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679584.1"
},
{
"aa_ref": "S",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "c.212G>T",
"hgvs_p": "p.Ser71Ile",
"transcript": "ENST00000959479.1",
"protein_id": "ENSP00000629538.1",
"transcript_support_level": null,
"aa_start": 71,
"aa_end": null,
"aa_length": 333,
"cds_start": 212,
"cds_end": null,
"cds_length": 1002,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000959479.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "n.*76G>T",
"hgvs_p": null,
"transcript": "ENST00000681512.1",
"protein_id": "ENSP00000505903.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000681512.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"hgvs_c": "n.*76G>T",
"hgvs_p": null,
"transcript": "ENST00000681512.1",
"protein_id": "ENSP00000505903.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000681512.1"
}
],
"gene_symbol": "CTSW",
"gene_hgnc_id": 2546,
"dbsnp": "rs1461461985",
"frequency_reference_population": 6.8406e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8406e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08808577060699463,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.117,
"revel_prediction": "Benign",
"alphamissense_score": 0.1283,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.023,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001335.4",
"gene_symbol": "CTSW",
"hgnc_id": 2546,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.341G>T",
"hgvs_p": "p.Ser114Ile"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}